Nomad and/or CM not starting job at Zero

I am having a problem with jobs starting several millimeters above the just set zero point. Once I commit the job to run, the spindle rises up several millimeters, then begins the process of homing, spinning up the spindle etc. When the bit goes to return to zero to start the job, it returns to that point the spindle raised up to, not the set zero point and then starts cutting in air. If I was deep cutting I could just cheat and add depth to the thickness of the material, but I am trying to do fine engraving and the job never reaches the work piece.

Has anyone else experienced this issue and found a resolution?

I am using CC to create the GCode using the latest beta build and running CM also using the latest (April 2016) build.